Database sequence homology amino acid. Medical search. Frequent questions

InterPro is a database of protein families, protein domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them. (wikipedia.org)
Information regarding which signatures significantly match these proteins are calculated as the sequences are released by UniProtKB and these results are made available to the public (see below). (wikipedia.org)
The matches of signatures to proteins are what determine how signatures are integrated together into InterPro entries: comparative overlap of matched protein sets and the location of the signatures' matches on the sequences are used as indicators of relatedness. (wikipedia.org)
InterPro also includes data for splice variants and the proteins contained in the UniParc and UniMES databases. (wikipedia.org)
CDD Conserved Domain Database is a protein annotation resource that consists of a collection of annotated multiple sequence alignment models for ancient domains and full-length proteins. (wikipedia.org)
MobiDB MobiDB is database annotating intrinsic disorder in proteins. (wikipedia.org)
PIRSF Protein classification system is a network with multiple levels of sequence diversity from superfamilies to subfamilies that reflects the evolutionary relationship of full-length proteins and domains. (wikipedia.org)
AbiQ has no homology to known or deduced proteins in the databases. (omicsdi.org)
The submitted sequences may reflect pathogen evolution during the course of the outbreak but the majority of the encoded proteins from these genomes may be identical to each other. (stackexchange.com)
By representing identical proteins using a single non-redundant protein accession number (with the prefix 'WP_'), redundancy in the database is significantly reduced. (stackexchange.com)
Their amino acid sequences suggest that they are mainly cytosolic or nuclear proteins partly associating with membranes (Talbot et al. (springer.com)
2009 ). The designated dysbindin paralogs show very limited sequence homology which raised the question whether DBNDD1 and DBNDD2 are dysbindin-like proteins or proteins that share a less conserved domain with DTNBP1 in the context of otherwise unrelated sequences (Ghiani and Dell'Angelica 2011 ). (springer.com)
As an outcome human DBNDD1 revealed a high sequence identity to dysbindin domain-containing proteins from other Hominidae (e.g. (springer.com)
Proteins with high sequence identity to human DBNDD1 can also be found in evolutionarily more distant species (e.g. (springer.com)
Traditionally, prediction of the functions of bacterial proteins is carried out for poorly studied molecules or hypothetical proteins predicted based on these genome sequences. (custom-essay.org)
With the growth of the structure database, such modelling becomes possible for more and more proteins. (custom-essay.org)
We identified zebrafish and Fugu TNFSF 13b homologues by genomic DNA database searches and determined that the predicted proteins share 68% and 76% sequence identity with trout TNFSF 13b. (usda.gov)
The 37-Mb genome was predicted to contain a total of 12,074 genes encoding proteins with a length greater than 100 amino acid residues (see Methods). (nature.com)
There are 43369 ZnF_U1 domains in 17228 proteins in SMART's nrdb database. (embl.de)
The individual databases for each protein can be accessed by clicking the proteins in the Figure. (lu.se)
They usually appear in multidomain proteins, together with catalytic domains, or other protein binding modules, such as Src homology 3 (SH3), phosphotyrosine binding (PTB) or pleckstrin homology (PH) domains. (lu.se)
Our analysis has been the amino acid sequences in proteins differ from what is carried out using two different methods, which differ substantially expected from random sequences in a statistically significant from what is used in ref. 3, although the starting point is similar. (lu.se)
PROT data base (6) of functional proteins, this method yields model containing only two amino acid types, hydrophobic and clear evidence for nonrandomness. (lu.se)
To under- denoted the AB model, consists of chains of two kinds of stand the statistical distribution of hydrophobicity along proteins ``amino acids'' interacting with Lennard-Jones potentials. (lu.se)

We have sequenced so far 29 amino acid residues of the SQR NH2 terminus and found that from the second residue, this sequence contains the highly conserved fingerprint of the NAD/FAD-binding domain of many NAD/FAD-binding enzymes (Wierenga, R. K., Terpstra, P., and Hol, W. G. S. (1986) J. Mol. (agri.gov.il)
These variants convergently acquired amino acid substitutions at critical residues in the spike protein, including residues R346, K444, L452, N460, and F486. (bvsalud.org)
The Src homology 2 (SH2) domains are about 100 residues in length with an average of 28% pairwise residue identity (Pfam code PF00017). (lu.se)
SH2 domains mediate intramolecular recognition and intermolecular protein-protein association almost invariably by binding to phosphorylated tyrosine (pY) residues in specific sequence contexts. (lu.se)
For sequences with a typical fraction of hydrophobic residues, we impact on how permissive with respect to sequence specificity find that the nonrandomness can be interpreted as anticorrela- the protein folding process is-- only sequences with nonran- tions. (lu.se)

The Human Genome Variation Society (HGVS) has established a sequence variant nomenclature , an international standard used to report variation in genomic, transcript and protein sequences. (ucsc.edu)
As a sub-objective, since PDE10A transcript variants were reported strictly through analyses of bovine genomic sequence, we also wanted to determine the nucleotide and amino acid sequences by experimental evidence. (plos.org)
Now, the genomic sequencing of organisms promises to be a major contributor to this field. (rupress.org)
Three introns were identified in the rainbow trout, Atlantic salmon and zebrafish genomic sequences, and the intron locations correspond closely to those in the mammalian TNFSF 13b genes. (usda.gov)
Systematic comparison of these homologous sequences resulted in identification of a conserved syntenic genomic island consisting of up to 33 core genes in 16 beta- and gamma-Proteobacteria. (ox.ac.uk)
These diverse genomic islands shared a common evolutionary origin, insert into tRNA genes, and have diverged widely, with G+C contents ranging from 40 to 70% and amino acid homologies as low as 20 to 25% for shared core genes. (ox.ac.uk)

Sequence analysis showed significant homology to zebra fish, sea urchin and human 17b-HSD. (molcells.org)
Comparison of the Cry1Ia1 amino acid sequence to known amino acid sequences revealed no significant homology to known toxins or known allergens. (ashs.org)

We performed a Basic Local Alignment Search Tool (BLAST) analysis to identify regions of local similarity between the human DBNDD1 and protein sequences from other species (Fig. 1 ). (springer.com)
Sequence alignment [Clustal Omega (Madeira et al. (springer.com)
Areas covered include sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases and subcellular localization prediction. (lu.se)

The source of information for the prediction can be the homology of nucleotide sequences, gene expression profiles or phylogenetic and phenotypic profiles. (custom-essay.org)

This problem is magnified in organisms that have their genomes sequenced for the first time ( Fig. 1c ). (nature.com)
Silver Age of GOLD Introduces New Features The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives. (doe.gov)
The Q33 and BM13 genomes exhibit homology, not only to P335-type, but also to elements of the 936-type phage sequences. (omicsdi.org)
Because a non-redundant protein sequence may be found in RefSeq genomes from multiple species, the organism information provided on the protein record reflects the lowest-common taxonomic node ranging from the genus species level to super-kingdom . (stackexchange.com)
More than 37,000 high-quality ESTs, excluding sequences of mitochondrial genome, microbial genomes, and rDNA, have been produced from 18 libraries of various BPH tissues and stages. (biomedcentral.com)

The primary PIRSF classification unit is the homeomorphic family, whose members are both homologous (evolved from a common ancestor) and homeomorphic (sharing full-length sequence similarity and a common domain architecture). (wikipedia.org)
In the case of protein similarity search, we propose to decrease the index size by reducing the amino acid alphabet. (biomedcentral.com)
Translated partial amino acid sequence of pln A gene in MCC4246 displayed 48 amino acid sequences showing 100% similarity with plantaricin A of Lactobacillus plantarum (WP_0036419). (researchsquare.com)

Genome sequence was partly determined, and phylogenetic studies were conducted. (cdc.gov)
Viral RNA was amplified for phylogenetic studies by using ONNV-specific primers for nsP3, E2, and E1 sequences (primer sequences are available on request). (cdc.gov)

These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function (human-curated molecular function and biological process classifications and pathway diagrams), as well as inference of amino acids important for functional specificity. (wikipedia.org)
permissive with respect to sequence specificity the protein folding process is, we have carried out the same analysis for a Section 1: Introduction toy model (7, 8), for which unbiased samples of folding and Hydrophobicity is widely believed to play a central role in the nonfolding sequences can be obtained. (lu.se)

0.05, the evolutionary substitution database must contain at least 3(M) variants, where M equals the number of codons in the gene. (nih.gov)
These data validate our hypothesis that detailed evolutionary analyses help predict the consequences of missense amino-acid variants. (nih.gov)
Zou and Xiao (2016) deployed three variants of the famous feature, Pseudo Amino Acid Composition (PseAAC), and the multi-label KNN algorithm. (frontiersin.org)

Based on these previous analyses and clinical findings, CLRN1 was directly sequenced in 17 patients susceptible to carrying mutations in this gene. (molvis.org)
We report evidence from cDNA isolation and expression analysis as well as analyses of genome, expressed sequence tag (EST), cDNA and expression databases for a new gene named SPRN (shadow of prion protein). (nih.gov)
He has published numerous original ideas and reports, established standards and guidelines for variations and variation databases and developed tools and performed analyses for the interpretation of variations in several diseases. (lu.se)

The virion acts in the synaptic space, where homology in amino acid sequences between neurotransmitter receptors for acetylcholine, GABA, and glycine may afford a mechanism for viral binding of these receptors. (medscape.com)

The fish and mammalian sequences are also well conserved, particularly for zebrafish, to beyond the end of the hydrophobic sequence (identity 41-53%, 78 amino acids, zebrafish length). (nih.gov)
Database information indicates expression of SPRN in embryo, brain and retina of mouse and rat, hippocampus of human, and in embryo and retina of zebrafish, and we directly confirmed a strikingly specific expression of the mammalian (human, mouse, rat) transcripts in whole brain. (nih.gov)

c), Number of reactions KEGG added or removed for selected organismal networks over the course of the same period for two recently sequenced organisms. (nature.com)
Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. (peerj.com)
10 kDa in size with 37-48 amino acids that inhibit growth of food spoilage organisms such as Listeria monocytogenes, Bacillus cereus, Clostridium perfringens, Staphylococcus aureus and E. coli (Rodrigues et al. (researchsquare.com)

Sequence analysis of this fragment revealed a complete open reading frame (abiQ), which encodes a putative protein of 183 amino acids. (omicsdi.org)
A variety of approaches, including biochemical purification, gene isolation by homology, and genetic screens, have been successfully used for the identification of putative protein kinases and phosphatases. (rupress.org)

Here, we present the complete genome sequences of two P335-type phages, Q33 and BM13, isolated in North America and representing a novel lineage within this phage group. (omicsdi.org)

These are available as position-specific score matrices (PSSMs) for fast identification of conserved domains in protein sequences via RPS-BLAST. (wikipedia.org)

We calculated p16 evolution using amino acid substitution matrices and nucleotide substitution distances. (nih.gov)
The current p16 evolutionary substitution database is too small to determine whether observations of 'absolute conservation' are statistically significant. (nih.gov)

Methods A next-generation sequencing (NGS) panel was created for the human TRPV1 gene and in addition, for the leukotriene receptors BLT1 and BLT2 recently described to modulate TRPV1 mediated sensitisation processes rendering the coding genes LTB4R and LTB4R2 important co-players in pharmacogenetic approaches involving TRPV1. (researchgate.net)
The NGS workflow was based on a custom AmpliSeq™ panel and designed for sequencing of human genes on an Ion PGM™ Sequencer. (researchgate.net)
A cohort of 80 healthy subjects of Western European descent was screened to evaluate and validate the detection of exomic sequences of the coding genes with 25 base pair exon padding. (researchgate.net)
This identified approximately 140 chromosome loci where nucleotides deviated from the reference sequence GRCh37 hg19 comprising the three genes TRPV1, LTB4R and LTB4R2. (researchgate.net)
It is suitable for large-scale sequencing of TRPV1 and functionally related genes. (researchgate.net)
Among the top ten most abundantly expressed genes, three are unique and show no homology in BLAST searches. (biomedcentral.com)
With the exception of late blight resistance, the other novel traits (i.e. reduced asparagine levels, lower levels of reducing sugars, and reduced black spot bruising) are achieved through the transcription of inverted repeat sequences containing small fragments of DNA from five different endogenous genes (i.e. (canada.ca)
METHODS: To identify expressed TNFSF genes, we searched a computer database of ~50,000 rainbow trout expressed sequence tags generated at the National Center for Cool and Cold Water Aquaculture. (usda.gov)
The blocks of A. oryzae -specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. (nature.com)
Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation. (nature.com)

Amino acid sequence analysis of six tryptic peptides of PRP 1 followed by homology search in a protein sequence data base revealed 100% identity of all six peptides with the deduced amino acid sequence of human calpactin I heavy chain. (nebraska.edu)
Expressed sequence tag (EST) analysis and related applications are useful to elucidate the mechanisms of resistance and virulence and to reveal physiological aspects of this non-model insect, with its poorly understood genetic background. (biomedcentral.com)
Combining deep sequencing and bioinformatics analysis, the percent of the common sequences in total sRNAs was 92.79%, but the number of unique sRNAs in the flying queens was more than that in non-flying queens. (chinaagrisci.com)
Syntenic analysis of the three aspergilli revealed the presence of syntenic blocks and A. oryzae -specific blocks of sequence (lacking synteny with the two other aspergilli) in a mosaic manner throughout the A. oryzae genome ( Fig. 1 ). (nature.com)
Bioinformatics analysis of the complete sequence of a typical H. influenzae conjugative resistance element, ICEHin1056, revealed the shared evolutionary origin of this element. (ox.ac.uk)
This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). (cdc.gov)
METHODS: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. (cdc.gov)
In this way, the analysis is more sensitive to teins in the SWISS-PROT data base, convincingly show that long-range correlations along the sequence. (lu.se)
wavelength corresponding to -helix structure, as one might have statistical analysis on the sequences that fold well indicates expected, but also at large wavelengths. (lu.se)

Conclusions Results suggested that the NGS approach based on AmpliSeq™ libraries and Ion Personal Genome Machine (PGM) sequencing is a highly efficient mutation detection method. (researchgate.net)

In this paper, we focus on massive protein sequence comparisons: a large database is iteratively compared with relatively short queries (such as newly sequenced data). (biomedcentral.com)

Many sequences-particularly bacterial sequences-are identical between various different species so having a separate RefSeq entry for each of them would be inefficient. (stackexchange.com)

2019 ) was used, https://www.ebi.ac.uk/Tools/msa/clustalo/ ] of human DBNDD1 and similar protein sequences found by a BLAST search in other selected species. (springer.com)
This type of method is called template-based modelling: templates can be found through comparison of amino acid sequences in software BLAST (in particular, BlastP), using text format FASTA. (custom-essay.org)

Despite the small p16 sequence database, our calculations of high conservation correctly predicted loss of cell cycle arrest function in 75% of tested codons, and low conservation correctly predicted wild-type function in 80-90% of codons. (nih.gov)
But having a short sequence of 241aa in several sequence might indicate good conservation (maybe it is a domain? (stackexchange.com)
The sequence conservation of the putative dysbindin domain across all selected species is notable (Fig. 1 shaded region). (springer.com)

In contrast to usual matrices, these matrices are rectangular since they compare amino acid groups from different alphabets. (biomedcentral.com)

Additionally, we compare the annotation behavior of current database curation efforts with our predictions and find that curation efforts are biased towards adding (rather than removing) reactions to organismal networks. (nature.com)

The gene has an open reading frame (ORF) of 918 nucleotides coding for a polypeptide of 306 amino acids and a calculated mass of 35-kDa. (molcells.org)

National Centre for Biotechnology Information, the CAB ferences between the major pathogen groups--viruses, International Bioscience database of fungal names, and bacteria, fungi, protozoa, and helminths. (cdc.gov)

The RT-PCR product was sequenced (GenBank accession no. (cdc.gov)

When the accuracy of genus predictions was averaged over a representative range of identities with the reference database (100%, 99%, 97%, 95% and 90%), all tested methods had ≤50% accuracy on the currently-popular V4 region of 16S rRNA. (peerj.com)
In these papers, accuracy is defined as the fraction of sequences that are correctly classified at each rank (see Acc RDP in Methods). (peerj.com)
To reveal amino acid followers, -helix and -sheet location, as a rule, computer programming methods are used. (custom-essay.org)

2021 ). The human DBNDD1 isoforms 1 (UniProtKB: Q9H9R9-1) and 2 (UniProtKB: Q9H9R9-2) differ only in the N-terminal region where 20 amino acids are additional in isoform 2. (springer.com)
In contrast, isoform 3 (UniProtKB: Q9H9R9-3) carries a 100 amino acids long N-terminal sequence extension. (springer.com)

After CLRN1 sequencing, we found two novel mutations, p.R207X and p.I168N. (molvis.org)
With the V4 region, 95% identity was found to be a twilight zone where taxonomy is highly ambiguous because the probabilities that the lowest shared rank between pairs of sequences is genus, family, order or class are approximately equal. (peerj.com)
A fundamental step in such studies is to predict the taxonomy of sequences found in the reads. (peerj.com)
A homologue of HSD was found in the EST database of Ciona intestinalis and cloned. (molcells.org)
My sequence had 241 amino acids and I found a lot of sequences with 100% identity, 100% cover and 0 E-value exactly the same as my sequence but with different IDs. (stackexchange.com)

RESULTS: Here, we report the characterization of a cDNA, 1RT126I22, which contains a TNF homology domain. (usda.gov)

A valid method for introducing molecular studies into insects without a genetic background is construction of an EST database. (biomedcentral.com)

We predict organismal metabolic networks using sequence homology and a global metabolic network constructed from all available organismal networks. (nature.com)
We show, however, that when homology is used with a global metabolic network one is able to predict organismal metabolic networks that have enhanced network connectivity. (nature.com)

Amino acid substitutions comprise the most common mutational event. (lu.se)

cfSNV can accurately detect mutations in cfDNA even with medium-coverage (e.g., ≥200×) sequencing, which makes whole-exome sequencing (WES) of cfDNA a viable option for various clinical utilities. (bvsalud.org)

Show us your query sequence and a few of the redundant results. (stackexchange.com)
Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. (cdc.gov)

Increasing the number of sequences from three to seven significantly improved the predictive value of evolutionary computations. (nih.gov)

LNO was used to evaluate coverage, defined as the fraction of sequences that are classified, without attempting to assess whether predictions are correct. (peerj.com)

We propose a practical index size reduction of the neighborhood data, that does not negatively affect the performance of large-scale search in protein sequences. (biomedcentral.com)
by homology]Input DNA Sequence or Amino acid sequence and select homology search program, then push 'Search' button. (medals.jp)

While sequence homology has been a standard to annotate metabolic networks it has been faulted for its lack of predictive power. (nature.com)

A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)

I assessed the accuracy of several algorithms using cross-validation by identity, a new benchmark strategy which explicitly models the variation in distances between query sequences and the closest entry in a reference database. (peerj.com)

There are many superfamilies of Znf motifs, varying in both sequence and structure. (embl.de)

In this regard, antimicrobial peptides or the bacteriocins from food grade lactic acid bacteria (LAB) have engrossed because of their safety and broad range of antibacterial spectrum. (researchsquare.com)

Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity. (wikipedia.org)
The relationship between identity and taxonomy was quantified as the probability that a rank is the lowest shared by a pair of sequences with a given pair-wise identity. (peerj.com)
The trout TNFSF 13b predicted protein shares 54% amino acid identity with human and chicken TNFSF 13b, and 51% identity with mouse TNFSF 13b. (usda.gov)

2021 ), https://pfam.xfam.org/ ] predicts human DBNDD1 mainly as an intrinsically disordered protein (IDP) and also the recently released AlphaFold database (Jumper et al. (springer.com)

EC 4.3.1.5), enzyme catalyzing the conversion of L-phenylalanine to trans-cinnamic acid in the first step of phenylpropanoid pathway were conducted in the edible branchlets of broccoli during early postharvest senescence. (scialert.net)
By amino acid sequence homology, we have identified PRP 2 as the glycolytic enzyme 3-phosphoglycerate kinase. (nebraska.edu)

A typical comparison, for example, is to query a database with a newly discovered sequence. (biomedcentral.com)
Thus, in practice, the full dynamic programming approach is applied to comparison of short sequences. (biomedcentral.com)
Representation of the three stages of comparison of a query (vertical) against a database (horizontal): Stage 1: identify seeds, i.e. small patterns occurring in both the query and the database (black diagonals). (biomedcentral.com)

Anatomy12

Organisms18

Chemicals and Drugs88

Analytical, Diagnostic and Therapeutic Techniques and Equipment40

Phenomena and Processes87

Disciplines and Occupations4

Information Science18

Health Care3

Proteins24

Residues5

Genomic6

Significant homology2

Alignment3

Nucleotide sequences1

Genomes5

Similarity3

Phylogenetic2

Specificity2

Variants3

Analyses3

Synaptic1

Zebrafish2

Organisms3

Putative protein2

Genome sequences1

Conserved domains1

Substitution2

Genes10

Analysis9

Mutation1

Protein sequence1

Bacterial1

BLAST2

Conservation3

Matrices1

Annotation1

Nucleotides1

Pathogen1

Accession1

Methods3

UniProtKB2

Found5

CDNA1

Genetic1

Predict2

Comprise1

Mutations1

Show2

Evolutionary1

Predictions1

Search2

Predictive1

Data1

Variation1

Superfamilies1

Antimicrobial1

Identity3

Human1

Enzyme2

Comparison3